Hi,
I've built my little project using the Leostick, and so far I've always powered it from a USB port.
However for actual deployment, it'll be running off batteries.

I'm not clear on which pins I should be providing the 5V power to -- is it the one marked "VIN" or one of the ones marked 5V? (There is one 5V between AREF and RESET, and another one between 3.3V and Ground)

One particular thing that's relevant to your question is the note on the schematic about jumpering across the USB-PWR cut-track jumper. After the board was fully routed I added a thin track across that jumper, so even though it's shown as an open circuit in the schematic it's actually a closed circuit in production. That's deliberate, so that in normal use power can be taken from the USB connection.

However, in your case you *may* want to cut the thin track in the middle of that jumper, depending on how you'll be using it. If you connect an external regulated power supply to the 5V rail it would be best to cut that track so that when you plug it into your computer the power supply is not trying to supply power to the computer's USB port. It's quite likely that you'd be OK, but best to play it safe. However, that means you won't then be able to power the LeoStick from the USB port unless you solder back across the cut-track jumper.

The two headers labelled "5V" are connected on the PCB, so it doesn't matter which one you use.

You *could* feed power to VIN, but only if you don't cut the USB-PWR jumper and if you don't have it plugged into a USB port.

I hope that helps. It was a kinda complicated explanation, so if I didn't make sense please say so!
--
Jon